[English] 日本語
Yorodumi
- PDB-6odl: Crystal structure of GluN2A agonist binding domain with 4-butyl-(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6odl
TitleCrystal structure of GluN2A agonist binding domain with 4-butyl-(S)-CCG-IV
ComponentsGlutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
KeywordsTRANSPORT PROTEIN / NMDA RECEPTOR / ANTAGONIST / RECEPTOR
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / serotonin metabolic process ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / serotonin metabolic process / response to other organism / protein localization to postsynaptic membrane / cellular response to magnesium ion / regulation of ARF protein signal transduction / positive regulation of inhibitory postsynaptic potential / sleep / response to methylmercury / response to carbohydrate / locomotion / dendritic spine organization / response to manganese ion / regulation of NMDA receptor activity / conditioned place preference / cellular response to dsRNA / cellular response to lipid / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / spinal cord development / response to amine / parallel fiber to Purkinje cell synapse / cellular response to zinc ion / startle response / monoatomic cation transmembrane transport / dopamine metabolic process / modulation of excitatory postsynaptic potential / response to lithium ion / response to light stimulus / regulation of postsynaptic membrane potential / action potential / cellular response to glycine / positive regulation of excitatory postsynaptic potential / regulation of neuronal synaptic plasticity / positive regulation of protein targeting to membrane / cellular response to manganese ion / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / multicellular organismal response to stress / neuron development / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / glutamate-gated receptor activity / cell adhesion molecule binding / glutamate-gated calcium ion channel activity / neurogenesis / sensory perception of pain / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / cytoplasmic vesicle membrane / protein tyrosine kinase binding / hippocampus development / excitatory postsynaptic potential / regulation of membrane potential / learning / response to nicotine / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / response to cocaine / synaptic membrane / protein catabolic process / response to lead ion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / negative regulation of protein catabolic process / cerebral cortex development / visual learning / calcium ion transmembrane transport / regulation of synaptic plasticity / calcium channel activity / cellular response to growth factor stimulus / response to wounding / long-term synaptic potentiation / terminal bouton / memory / response to calcium ion / calcium-dependent protein binding / calcium ion transport
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-M7V / Glutamate receptor / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMou, T.C. / Clausen, R.P. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS097536 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Stereoselective synthesis of novel 2'-(S)-CCG-IV analogues as potent NMDA receptor agonists.
Authors: Maolanon, A. / Papangelis, A. / Kawiecki, D. / Mou, T.C. / Syrenne, J.T. / Yi, F. / Hansen, K.B. / Clausen, R.P.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
B: Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1384
Polymers62,7082
Non-polymers4302
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-14 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.094, 52.094, 197.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31353.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959, UniProt: G3V9C5
#2: Chemical ChemComp-M7V / (1S,2R)-2-[(S)-amino(carboxy)methyl]-1-butylcyclopropane-1-carboxylic acid


Mass: 215.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. obs: 22638 / % possible obs: 94.2 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rpim(I) all: 0.052 / Rrim(I) all: 0.125 / Net I/σ(I): 12
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.75 / Num. unique obs: 2296 / CC1/2: 0.596 / Rpim(I) all: 0.233 / Rrim(I) all: 0.482 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A5S

2a5s


Resolution: 2.3→19.026 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 1915 8.75 %
Rwork0.2243 --
obs0.2294 21886 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4420 0 0 170 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034522
X-RAY DIFFRACTIONf_angle_d0.766124
X-RAY DIFFRACTIONf_dihedral_angle_d7.4923207
X-RAY DIFFRACTIONf_chiral_restr0.247688
X-RAY DIFFRACTIONf_plane_restr0.003782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.35770.38191420.28891497X-RAY DIFFRACTION99
2.3577-2.42130.31471410.26151486X-RAY DIFFRACTION99
2.4213-2.49240.32131470.25051506X-RAY DIFFRACTION99
2.4924-2.57270.28671480.24431510X-RAY DIFFRACTION100
2.5727-2.66440.36351320.26081394X-RAY DIFFRACTION93
2.6644-2.77080.31941360.29491414X-RAY DIFFRACTION93
2.7708-2.89640.35261440.25681523X-RAY DIFFRACTION100
2.8964-3.04860.32291420.25451494X-RAY DIFFRACTION100
3.0486-3.23870.31971360.23251530X-RAY DIFFRACTION99
3.2387-3.48730.27251130.25471165X-RAY DIFFRACTION77
3.4873-3.83570.34331160.24681207X-RAY DIFFRACTION80
3.8357-4.38480.23931220.20291210X-RAY DIFFRACTION80
4.3848-5.50210.23911440.16741513X-RAY DIFFRACTION100
5.5021-19.02660.18831520.16681522X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more